Deep resequencing of Trichinella spiralis reveals previously un-described single nucleotide polymorphisms and intra-isolate variation within the mitochondrial genome.

Authors: Webb, Kristen; Rosenthal, Benjamin

Submitted to: Infection, Genetics and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/23/2009
Publication Date: 3/1/2010
Citation: Webb, K.M., Rosenthal, B.M. 2010. Deep resequencing of Trichinella spiralis reveals previously un-described single nucleotide polymorphisms and intra-isolate variation within the mitochondrial genome. Infection, Genetics and Evolution. 2:304-310.

Interpretive Summary: New methods of genome sequencing were applied to an isolate of the zoonotic parasite Trichinella spiralis in order to establish whether earlier ideas concerning its history of dissemination (based on partial sequencing of the mitochondrial genome) could be sustained in the light of comprehensive data, and in order to evaluate (for the first time) whether or not the genome of this organelle was uniform among larval worms collected from a given host. Doing so has affirmed and refined the concept that this parasite became adapted to domesticated swine and was introduced to the Americas from Europe; this work also shows, for the first time, that a single sequence oversimplifies the genetic complexity of isolates comprised of thousands or millions of parasitic larvae.

Technical Abstract: Trichinella spiralis is a parasitic roundworm that infects domestic swine, rats and humans. Ingestion of infected pork by humans can lead to the potentially fatal disease trichinellosis. The phylogeny and historical dispersal of Trichinella spp. have been studied, in part, by sequencing portions of the mitochondrial genome. Such studies rely on two untested beliefs: that variation in a portion is representative of the entire mitochondrial genome, and that each isolate is characterized by only one mitochondrial haplotype. We have used next generation DNA sequencing technology to obtain the complete mitochondrial genome sequence from a second isolate of T. spiralis. By aligning it to the only previously sequenced genome, we sought to establish whether the exceptionally deep sequencing coverage provided by such an approach could detect regions of the genome which had been misassembled, or nucleotide positions which may vary within an isolate. The new data broadly confirm the gene order and sequence assembly for protein coding regions. However, in the repetitive non-coding region, alignment to the previously published genome sequence proved difficult. Such discrepancies may represent true biological variation, but may rather result from methodological or algorithmic sources. Within the 13,902 bp protein-coding region, 7 polymorphisms were identified. Six of these polymorphisms occurred within protein coding genes and three alter an amino acid sequence, one occurred in a tRNA-Ile sequence, and four were found to vary within our isolate. Thus, comparing only two isolates of T. spiralis has enabled discovery previously unrecognized variation within the species. Characterizing diversity within and among the mitochondrial genomes of additional species of Trichinella would undoubtedly yield further insights into the diversification history of the genus. Our study affirms that next generation DNA sequencing technology can reliably characterize complete mitochondrial genomes.